Run the speaker wires from your amp to the speaker inputs of the sub. Now run a new pair of wires to your speakers from the sub's speaker outputs. Use the crossover & volume controls to match your speakers.
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Houstonreef, my understanding is that you are correct. Most would prefer to set up the sub in the way you described (essentially bi-wiring the sub and speakers from the integrated amp speaker outputs). You will probably need to adjust the highpass filter and volume of your sub to integrate with your speakers by using a sound meter and low frequency sweep CD/mp3. Once that is properly set up, you can forget about the sub and let your integrated amp take care of volume level. Maybe others can chime in.
There is an important difference between these if I understand your description. In the case of Bi wiring the two both will be running full range. If you send the signal from the sub I assume it will have the bottom frequencies going to the main speakers removed by the subs crossover. Both will work and the choice would be which sounds better to you. Disclaimer, I use the similar but not identical REL and am extrapolating from it.